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Thermal Fluctuations and Infrared Spectra of the Formamide–Formamidine Complex

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journal contribution
posted on 25.10.2012, 00:00 by Łukasz Walewski, Artur Smaga, Bogdan Lesyng, Joanna Sadlej
Combined effects of hydrogen bonding and thermal fluctuations on the structure and infrared spectra of the formamide–formamidine dimer, FM···FI, are studied using ab initio molecular dynamics simulations. The equilibrium structure of the dimer is stabilized by two hydrogen bonds that form a pattern reminiscent of that found in the adenine-thymine base pair. The structure of the hydrogen bonds at 300 K is subject to large fluctuations, with the hydrogen atom being tightly bound to the donor in the covalent bonding scenario. The hydrogen bond acceptor has a tendency to detach farther away from the D–H pair, approaching the dimer dissociation limit. Moreover, the N–H···O hydrogen bond breaks occasionally, thus giving rise to an “open” structure of the dimer, while the N–H···N bond stays largely intact at this temperature. Thermal fluctuations result in the minor red shifts of the monomer vibrational frequencies indicative of the anharmonicity of the potential energy surface. In contrast, the IR frequencies of the two symmetric NH2 vibrational modes of the FM and FI monomers are shifted substantially toward the red upon hydrogen bond formation in the FM···FI dimer. Dynamical effects studied here are relevant, in particular, to the hydrogen bonding of nucleic acids at finite temperatures.